Hello Mohammad.
What exactly is meant by each of the two phrases depends on the context. Encrypted GRE Tunnel with IPSec refers to the encryption of the information sent over a GRE tunnel using the functionalities of IPSec. GRE over IPSec is not that specific and it depends on what the person speaking really means.
IPSec used in combination with GRE can function in two ways, either in tunnel mode, or transport mode.
Tunnel mode, which is the default, which is also what Rene has configured in the lesson, the whole GRE packet is encapsulated and encrypted within the IPSec packet.
Transport mode on the other hand, involves the encapsulation of only the GRE payload. The GRE header in this case is not encrypted.
Take a look at this post by Rene for more details.
I hope this has been helpful!
Laz